Nature Methods technological breakthrough: Use sound to "observe" a single cell?

If you are a researcher and want to understand how a few cells in a living body work, this is not a simple task
.
The human body contains about 37 trillion cells; the fruit flies flying around the overripe banana on your counter may have 50,000 cells
.
Even the tiny worm Caenorhabditis elegans commonly used in biological research has as many as 3000 cells
.
So, how to monitor a few of the tiny spots?

Scientists in the laboratory of Mikhail G.
Shapiro, a professor of chemical engineering at the California Institute of Technology and a researcher at the Institute of Traditional Medicine, have found a way
.

This new technology makes use of the so-called "sound reporter gene," and Shapiro is a pioneer in this area
.
To understand the sound reporter gene, we must first know that the reporter gene is a special piece of DNA that researchers can insert into the genome of an organism to help them understand the behavior of the organism
.
Historically, reporter genes have encoded fluorescent proteins
.
For example, if researchers insert one of these reporter genes next to the gene they want to study—for example, the gene responsible for neuron development—the activation of these neuronal genes will also produce fluorescent protein molecules
.
When the appropriate light shines on these cells, they will light up, just like marking a specific paragraph on a book with a highlighter
.

However, these fluorescent reporter genes have a big disadvantage: light cannot penetrate very far through living tissue
.

Therefore, Shapiro invented a reporter gene that uses sound instead of light
.
When these genes are inserted into the cell's genome, the cell produces tiny hollow protein structures called air sacs
.
These vesicles are usually found in certain types of bacteria.
They use vesicles to float in the water, but when ultrasound hits them, they also have a useful characteristic, that is, a "bell"
.

The idea is that when a cell that produces these vesicles is imaged by ultrasound, it will send out a sound signal announcing its existence, allowing researchers to see where it is and what it is doing
.
In previous work in Shapiro's lab, this technique was used to show the activity of enzymes in cells
.

In their latest paper, the research team describes how the technology’s sensitivity can be increased to such an extent that it is now possible to image individual cells carrying acoustic reporter genes in human tissues
.

Image source: Shapiro Laboratory, California Institute of Technology

"Compared with previous studies on gas vesicles, this paper allowed us to see a smaller number of gas vesicles," said first author Daniel Sawyer (21-year-old Ph.
D.
), a former bioengineering PhD student in Shapiro's laboratory
.
"It's like changing from a satellite that can see the lights of a small town to a satellite that can see the lights of a single lamp post
.
"

Their improvement shows that the sensitivity is more than 1,000 times higher than the previous technology, and they have been using this technology to image cells carrying acoustic reporter genes
.
The difference lies in the ultrasound they use and how the airbag responds to ultrasound
.

The previous imaging technique relied on the vesicles to make a sound like a bell being struck, while the new technology uses stronger ultrasound to make the vesicles "rupture" like a balloon
.

Shapiro said: "The vesicle produces a very strong signal at that moment
.
Then the vesicle will rupture and stop sending the signal
.
We are looking for that little light spot
.
"

This light spot is so clear that researchers can easily detect it, even in the background noise generated by ultrasound penetrating the tissue
.
Shapiro said that recent research on engineered strains of injectable bacteria that attack cancer cells or "tumor home" bacteria has created a better way to track these cells to understand where they are in the body
.
The researchers found that when bacteria are also designed to carry airbag genes, it is possible to track the process of individual bacterial cells entering and passing through the liver after being injected into the blood
.

If researchers want to use ultrasound to study the composition of the gut microbiota, this level of sensitivity is necessary
.
Once the gut microbiota is destroyed, it will affect diseases such as Alzheimer's and autism
.

He said: "There are many types of bacteria in your intestines.
Some bacteria are very rare.
You need something sensitive enough to see the few bacteria deep in your body
.
"

Will squeezing the vesicles in the cell hurt the cell? No, it's not true
.

"In short, the answer is no, and in most practical cases, the answer is no.
In some cases, very small single bacterial cells and a large number of these gas vesicles are injured, but if some of them It becomes less feasible and will not have much impact on the number of bacteria
.
In mammalian cells, we do not see negative effects
.
"

This research team is exploring two paths for their research
.
One approach will be based on more advanced imaging techniques that researchers have developed
.
This will involve engineering and testing new types of vesicles with different properties, such as vesicles that are easier to rupture, stronger vesicles, or smaller vesicles that can enter places where larger vesicles cannot
.
The other way is to find practical applications for the technology they developed
.

Shapiro said: "In the field of optical microscopy, the co-evolution of optical probes and microscopy technologies, such as two-photon microscopes and light-plate microscopes (both types of fluorescence microscopes)
.
The paper is part of the development of ultrasound simulation imaging technology
.
"

references

"Ultrasensitive ultrasound imaging of gene expression with signal unmixing" by Daniel P.
Sawyer, Avinoam Bar-Zion, Arash Farhadi, Shirin Shivaei, Bill Ling, Audrey Lee-Gosselin and Mikhail G.
Shapiro, 5 August 2021,  Nature Methods .

DOI: 10.